TY - JOUR AB - The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission. AU - Eggermann, Emmanuel AU - Bucurenciu, Iancu AU - Goswami, Sarit AU - Jonas, Peter M ID - 3317 IS - 1 JF - Nature Reviews Neuroscience TI - Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses VL - 13 ER - TY - JOUR AB - We introduce two-level discounted and mean-payoff games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted or mean-payoff game and the lower level game is a (undiscounted) reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. For both discounted and mean-payoff two-level games, we show the existence of pure memoryless optimal strategies for both players and an ordered field property. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted or mean-payoff games can be decided in NP ∩ coNP. We also give an alternate strategy improvement algorithm to compute the value. © 2012 World Scientific Publishing Company. AU - Chatterjee, Krishnendu AU - Majumdar, Ritankar ID - 3314 IS - 3 JF - International Journal of Foundations of Computer Science TI - Discounting and averaging in games across time scales VL - 23 ER - TY - JOUR AB - We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P's offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one. AU - Berberich, Eric AU - Halperin, Dan AU - Kerber, Michael AU - Pogalnikova, Roza ID - 3115 IS - 4 JF - Discrete & Computational Geometry TI - Deconstructing approximate offsets VL - 48 ER - TY - JOUR AB - Computing the topology of an algebraic plane curve C means computing a combinatorial graph that is isotopic to C and thus represents its topology in R2. We prove that, for a polynomial of degree n with integer coefficients bounded by 2ρ, the topology of the induced curve can be computed with bit operations ( indicates that we omit logarithmic factors). Our analysis improves the previous best known complexity bounds by a factor of n2. The improvement is based on new techniques to compute and refine isolating intervals for the real roots of polynomials, and on the consequent amortized analysis of the critical fibers of the algebraic curve. AU - Kerber, Michael AU - Sagraloff, Michael ID - 3331 IS - 3 JF - Journal of Symbolic Computation TI - A worst case bound for topology computation of algebraic curves VL - 47 ER - TY - JOUR AB - Arrays of vertically aligned ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires (NWs) were prepared by means of the combination of two solution-growth processes. First, single-crystal ZnO NWs with controlled n-type doping were grown on conducting substrates by a low-cost, high-yield and seed-free electrochemical route. These NWs were covered by a titanium oxide shell of tunable thickness mediating successive adsorption-hydrolysis-condensation steps. Using this atomic-layer growth procedure, titania shells with controlled thickness and the anatase TiO2 phase were obtained after sintering at 450 °C. Higher sintering temperatures resulted in the formation of ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs by the interdiffusion of Zn and Ti ions at the ZnO–TiO2 interface. The performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs towards photoelectrochemical (PEC) water splitting was investigated as a function of the titania shell thickness. Furthermore, the performance of such core–shell NWs as photoelectrodes in dye-sensitized solar cells was also characterized. The TiO2 presence at the ZnO : Cl surface promoted a two-fold increase on the produced photocurrent densities, probing their potential for PEC and optoelectronic applications. Electrochemical impedance spectroscopy was used to corroborate the lower resistance for charge transfer between the NWs and the electrolyte in the presence of the TiO2 shell. AU - Fan, Jiandong AU - Zamani, Reza AU - Fábrega, Cristina AU - Shavel, Alexey AU - Flox, Cristina AU - Ibáñez, Maria AU - Andreu, Teresa AU - López, Amtonio AU - Arbiol, Jordi AU - Morante, Joan AU - Cabot, Andreu ID - 346 IS - 41 JF - Journal of Physics D: Applied Physics TI - Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness VL - 45 ER - TY - JOUR AB - The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently, we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper, we prove that this quotienting yields a sufficient condition for weak lumpability (that is to say that the quotient system is still Markovian for a given set of initial distributions) and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system (which means that the conditional probability of being in a given state in the original system knowing that we are in its equivalence class is an invariant of the system). We illustrate the framework on a case study of the epidermal growth factor (EGF)/insulin receptor crosstalk. AU - Feret, Jérôme AU - Henzinger, Thomas A AU - Koeppl, Heinz AU - Petrov, Tatjana ID - 3168 JF - Theoretical Computer Science TI - Lumpability abstractions of rule based systems VL - 431 ER - TY - JOUR AB - The potential to control the composition and crystal phase at the nanometer scale enable the production of nanocrystalline materials with enhanced functionalities and new applications. In the present work, we detail a novel colloidal synthesis route to prepare nanoparticles of the ternary semiconductor Cu2GeSe3 (CGSe) with nanometer-scale control over their crystal phases. We also demonstrate the structural effect on the thermoelectric properties of bottom-up-prepared CGSe nanomaterials. By careful adjustment of the nucleation and growth temperatures, pure orthorhombic CGSe nanoparticles with cationic order or polytypic CGSe nanoparticles with disordered cation positions can be produced. In this second type of nanoparticle, a high density of twins can be created to periodically change the atomic plane stacking, forming a hexagonal wurtzite CGSe phase. The high yield of the synthetic routes reported here allows the production of single-phase and multiphase CGSe nanoparticles in the gram scale, which permits characterization of the thermoelectric properties of these materials. Reduced thermal conductivities and a related 2.5-fold increase of the thermoelectric figure of merit for multiphase nanomaterials compared to pure-phase CGSe are systematically obtained. These results are discussed in terms of the density and efficiency of phonon scattering centers in both types of materials. AU - Ibáñez, Maria AU - Zamani, Reza AU - Li, Wenhua AU - Cadavid, Doris AU - Gorse, Stéphane AU - Katchoi, Nebll AU - Shavel, Alexey AU - López, Antonioo AU - Morante, Joan AU - Arbiol, Jordi AU - Cabot, Andreu ID - 377 IS - 23 JF - Chemistry of Materials TI - Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials VL - 24 ER - TY - JOUR AB - We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications. AU - Chatterjee, Krishnendu AU - Henzinger, Thomas A ID - 3846 IS - 2 JF - Journal of Computer and System Sciences TI - A survey of stochastic ω regular games VL - 78 ER - TY - JOUR AB - In this Letter we present detailed study of the density of states near defects in Bi 2Se 3. In particular, we present data on the commonly found triangular defects in this system. While we do not find any measurable quasiparticle scattering interference effects, we do find localized resonances, which can be well fitted by theory once the potential is taken to be extended to properly account for the observed defects. The data together with the fits confirm that while the local density of states around the Dirac point of the electronic spectrum at the surface is significantly disrupted near the impurity by the creation of low-energy resonance state, the Dirac point is not locally destroyed. We discuss our results in terms of the expected protected surface state of topological insulators. © 2012 American Physical Society. AU - Alpichshev, Zhanybek AU - Biswas, Rudro AU - Balatsky, Alexander AU - Analytis, James AU - Chu, Jiunhaw AU - Fisher, Ian AU - Kapitulnik, Aharon ID - 387 IS - 20 JF - Physical Review Letters TI - STM imaging of impurity resonances on Bi 2Se 3 VL - 108 ER - TY - JOUR AB - The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation. AU - Dai, Mingqiu AU - Zhang, Chen AU - Urszula Kania AU - Chen, Fang AU - Xue, Qin AU - McCray, Tyra AU - Li, Gang AU - Qin, Genji AU - Wakeley, Michelle AU - Terzaghi, William AU - Wan, Jianmin AU - Zhao, Yunde AU - Xu, Jian AU - Jirí Friml AU - Deng, Xing W AU - Wang, Haiyang ID - 3110 IS - 6 JF - Plant Cell TI - A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis VL - 24 ER -